New gene association measures by joint network embedding of multiple gene expression datasets
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Wenbo Guo | Guiying Wu | Jin Gu | Xiangyu Li | Zheng Wei | Tao Hu | J. Gu | Wenbo Guo | Jin Gu | Xiangyu Li | G. Wu | Tao Hu | Zheng Wei
[1] E. Sprinzak,et al. Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. , 1999, Genome research.
[2] Yudong D. He,et al. Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.
[3] Michael Griffin,et al. Gene co-expression network topology provides a framework for molecular characterization of cellular state , 2004, Bioinform..
[4] R. Strohman,et al. Maneuvering in the Complex Path from Genotype to Phenotype , 2002, Science.
[5] Jugal K. Kalita,et al. Reconstruction of gene co-expression network from microarray data using local expression patterns , 2014, BMC Bioinformatics.
[6] M. Yuan,et al. Model selection and estimation in the Gaussian graphical model , 2007 .
[7] Sara Ballouz,et al. Exploiting single-cell expression to characterize co-expression replicability , 2016, Genome Biology.
[8] Lin Song,et al. Comparison of co-expression measures: mutual information, correlation, and model based indices , 2012, BMC Bioinformatics.
[9] R. Tibshirani,et al. Sparse inverse covariance estimation with the graphical lasso. , 2008, Biostatistics.
[10] Mingzhe Wang,et al. LINE: Large-scale Information Network Embedding , 2015, WWW.
[11] Sara Ballouz,et al. Guidance for RNA-seq co-expression network construction and analysis: safety in numbers , 2015, Bioinform..
[12] Haiyan Huang,et al. Review on statistical methods for gene network reconstruction using expression data. , 2014, Journal of theoretical biology.
[13] Alexander J. Smola,et al. Reducing the sampling complexity of topic models , 2014, KDD.
[14] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[15] Thomas Craig,et al. GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases , 2012, BMC Genomics.
[16] Daniel A. Chamovitz,et al. Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network , 2009, BMC Systems Biology.
[17] Hong Yan,et al. Differential network analysis from cross-platform gene expression data , 2016, Scientific Reports.
[18] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[19] Paul Pavlidis,et al. The role of indirect connections in gene networks in predicting function , 2011, Bioinform..
[20] O. Alter,et al. A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms , 2011, PloS one.
[21] Stephen J. Wright,et al. Hogwild: A Lock-Free Approach to Parallelizing Stochastic Gradient Descent , 2011, NIPS.
[22] Laurin A. J. Mueller,et al. Integrative Network Biology: Graph Prototyping for Co-Expression Cancer Networks , 2011, PloS one.
[23] L. Foster,et al. Evaluating measures of association for single-cell transcriptomics , 2019, Nature Methods.
[24] Qiaozhu Mei,et al. PTE: Predictive Text Embedding through Large-scale Heterogeneous Text Networks , 2015, KDD.
[25] David Warde-Farley,et al. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function , 2008, Genome Biology.
[26] Sarah A. Teichmann,et al. Computational approaches for interpreting scRNA‐seq data , 2017, FEBS letters.
[27] Patrick Danaher,et al. The joint graphical lasso for inverse covariance estimation across multiple classes , 2011, Journal of the Royal Statistical Society. Series B, Statistical methodology.
[28] Daphne Koller,et al. Sharing and Specificity of Co-expression Networks across 35 Human Tissues , 2014, PLoS Comput. Biol..
[29] Su-In Lee,et al. Efficient Dimensionality Reduction for High-Dimensional Network Estimation , 2014, ICML.
[30] Jeffrey Dean,et al. Distributed Representations of Words and Phrases and their Compositionality , 2013, NIPS.
[31] D. Botstein,et al. Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[32] Michael Q. Zhang,et al. Network embedding-based representation learning for single cell RNA-seq data , 2017, Nucleic acids research.
[33] Alexandre d'Aspremont,et al. Model Selection Through Sparse Max Likelihood Estimation Model Selection Through Sparse Maximum Likelihood Estimation for Multivariate Gaussian or Binary Data , 2022 .
[34] Cheng Zhang,et al. Investigating the Combinatory Effects of Biological Networks on Gene Co-expression , 2016, Frontiers in physiology.
[35] Enrico Petretto,et al. Multi-tissue Analysis of Co-expression Networks by Higher-Order Generalized Singular Value Decomposition Identifies Functionally Coherent Transcriptional Modules , 2014, PLoS genetics.
[36] João Pedro de Magalhães,et al. GeneFriends: a human RNA-seq-based gene and transcript co-expression database , 2014, Nucleic Acids Res..
[37] S. Horvath,et al. Statistical Applications in Genetics and Molecular Biology , 2011 .
[38] Benjamin A. Logsdon,et al. Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer , 2016, bioRxiv.
[39] F. Azuaje,et al. Analysis of a gene co-expression network establishes robust association between Col5a2 and ischemic heart disease , 2013, BMC Medical Genomics.